Shadow the Hedgehog:Fanfic Version
by sonicshadowlover13
Summary: Based on the game. Shadow haven't recovered his memories, but he is gaining one of them, and the only way to regain those memories is from the strange alien, Black Doom. There are different sides to choose from the black hedgehog. Hero or villain? What path Shadow would follow?
1. Chapter 1

***Prologue***

***6 months after the defeat of Metal Sonic***

Outside the city of Station Square, the sun is setting behind the buildings, and birds were flying in the sky. Everything is so quiet and peaceful after Metal Sonic had been beaten by the heroes. But more importantly, only one "hero" is not with the others since. Not far from the city at the fields, there is a black hedgehog with red stripes by the oak tree on the hill with his arms crossed. In the black hedgehog's mind is like a train wreck. All he remembered is his name and the image inside his head.  
_  
'Shadow the Hedgehog...'_ The black hedgehog thought in mind. _'Why does that name haunt me? It's the only thing I can remember. And that gruesome image...'_ He shuts his eyes tight as he recalls the memory again.

* * *

**_*50 years ago*  
_**  
_Shadow is running down the corridor with the little girl with blonde hair, wearing a blue dress and a blue headband. The girl gripped onto Shadow's hand tight, and her face looks...terrified. Tears were falling from her eyes as they ran down the corridors of a place. Voices were heard behind the girl and the hedgehog, but they both ignored them and continued running._

_"They went this way!" One of the male voices says. "After them! Kill the creature!"_

_"The little girl was helping it escape! Take her down!" The other says._

_Next thing, the girl turned to the figure who had a gun in his hand and point it at her. The girl stood frozen, and then the gunshot was heard, and Shadow's cry is heard as well when everything turned white..._  
_  
"MARIA!"_

* * *

Shadow opened his eyes and look up at the orange and pink sky. He doesn't know what else think besides the horrible memory. Questions came to him.

"Who am I...and why can't I remember anything? And...who is this Maria?" He asked. After a moment, everything turned dark, and red... Shadow looked up at the sky again and saw unusual red clouds coming towards the city, then it made the opening center, coming down is strange creatures that are black and red with marks. Roaring is heard, and screaming in the city. Shadow watched with a calm look. "Hmm... Look how pathetic they are! I don't have time for these humans." He said by turning back to leave the fields.

"Shadow..." A deep, monstrous voice called out faintly. Shadow stopped where he was, making a look, now turning back and then saw a hologram of the alien. Behind it, there is a purple alien with tentacles and one eye.

"As you can see, the day of reckoning will soon be here." The hologram alien said. "Find the seven Chaos Emeralds, and bring them to me as promised."

"Huh? Who are you and how do you know I'm Shadow? And what are you talking about?" Shadow asked with a half shrug. But the creature didn't answer. He disappeared. Shadow is about to call out, the bombs around him exploded, but the hedgehog didn't care about that. "Just what was that all about?" He asked. "If he says he knows the truth about who I am...then like it or not, I have to believe him. The only way is to get the secrets of my past is to get those Chaos Emeralds." Shadow then hovered through the fields and went off to the city, that is about to be invaded.


	2. Chapter 2

***Chapter 1: Westopolis***

* * *

In the downtown of Westopolis, everyone were running away in fear of the black aliens who were now attacking and destroying everything. The GUN soliders arrived in ten jeeps, taking out their guns and shoot the aliens.  
Shadow arrived in the city, trying to find the alien that he had talked to before, about this "promise". What _DID_ Shadow promise him? Shadow had the amnesia for months and never recall anything about the promise he made for the alien leader. He only had the memories of a girl named Maria...who is she? Shadow shook his head to ignore the confusing thoughts, and focus on the mission that he suddenly had to do. He skates through the streets, passing humans and aliens, but then he heard a voice, a singing voice from the ally. Shadow's ear twitched as he heard it. He recognized the voice... Shadow went to the ally and found a blue hedgehog dancing there, wearing headphones and holding a white iPod. Sonic the Hedgehog is the name, a blue hero. He is singing a certain song.

_"I just want to fly._  
_Put your arms around me baby,_  
_Put your arms around me baby,_  
_I just want to fly._  
_Put your arms around me baby,_  
_Put your arms around me baby."_

Shadow watched him in annoyance. Did Sonic know that the city is being invaded now? If he did know, why is he being a dance-off at this time? Shadow picked up a beer bottle and threw it at Sonic's back. The blue hedgehog stopped singing and turned around. Shadow stares at Sonic in silent. Sonic took off his headphones and smiled at him.

"Hey Shadow! Long time no see!" He greeted. "What's going on, buddy?" Screaming and roaring is heard outside the ally. Sonic blinked and look up at the red sky. "Oooohh..." He says in a low voice.

"Some hero you are, Sonic." Shadow said in a tone. "You somehow bothered to be here alone, listen to your damn music, and never noticed something, huh?" Sonic's ears lowered a little.

"Why do you have to be so harsh to me, Shadow?" He asked. "Well, I have to go out there and save the world! C'mon, you can join me if you want!" Sonic ran passed Shadow in full speed. Shadow followed him out in the city. Before he could catch up with Sonic, a purple alien appeared in front of Shadow. It's the alien who made a hologram of the alien leader.

"You are late, Shadow..." It said. It's the same voice too. "From now on, my eye shall serve you for me."

"...Who are you?" Shadow asked in demand.

"No time for foolish questions, Shadow! Now, start finishing off these soldiers, who dare to defy me!" The alien said. "No one will defy me, Black Doom, the leader of the Black Arms!" Shadow stares at the one eye alien, blink a few times. Black Doom. So that's the leader. But, this here is the eye, Doom's Eye. And the rest of the black creatures are called, Black Arms. Shadow hears two soldiers ahead of him, trying to shoot the flying alien creatures. Shadow was told to kill the soldiers. But, why? Shadow just skates ahead and used Chaos Spear on them, making them fall on the ground, stunned. Doom's Eye made a chuckle, an evil chuckle. Shadow stares at the soldiers.

"Spare us!" One of them said. Doom's Eye flew beside Shadow.

"Make the humans suffer, Shadow!" He said. Before Shadow could say something, Sonic came back.

"Shadow?! What did you do to them?!" He asked. Sonic kneeled down by the GUN soldiers, giving them each a bottle of water. Doom's Eye got close to Sonic's face, like he was studying his features. "Whoa...who the heck are you?" Sonic asked.

"Hmmm... The blue hedgehog full of speed. And full of foolishness..." Doom's Eye said. Sonic glared at him in the eye.

"Hey! Watch it!" He snapped. "I don't know who you are, but what you all are doing is so stupid and wrong! We'll stop you, right Shadow?" Shadow turned to Sonic in silent. Doom's Eye wanted Shadow to destroy humans in the city, and Sonic wanted Shadow to save all humans and destroy the aliens. What will Shadow do? Hero or villain? Without saying a word, Shadow just skates off to the streets. Sonic called out his name and chase after the black hedgehog. Doom's Eye made a glare.

"Hmmm... He doesn't know what we were planning, does he?" He asked himself. "Perhaps Professor Gerald has done more to his memory than I imagined." He flew off to the different part of the city.

Shadow skates down the streets, but then he found something glowing ahead of him. He came close and realized that he found a green Chaos Emerald. Shadow picked it up and felt energy running through inside him. Not later though, Sonic arrived with a blue Chaos Emerald.

"There you are, Shadow! Look what I found from the aliens!" He said. Instantly, Shadow snatched it away from Sonic's hands. "Hey!" Sonic yelled.

"Once I find all the emeralds, I will uncover the truth about my past." Shadow said as he held to emeralds. Sonic blinked.

"God, you still don't remember a thing?" He asked. "But, you gotta remember, Shadow! We first met in San Francisco! It was a year ago! We-"

"Nothing comes up, Sonic!" Shadow told the blue hedgehog. "Although, one memory about the girl is there in my head. I don't know who she is... Something tells me that she knows me very well..." Sonic knew that Shadow is talking about his old friend, Maria Robotnik. Months ago, Sonic tried to make Shadow remember, but nothing rang a bell. Sonic thought Shadow should find out himself. If Sonic tries again, he knew that Shadow will rip him apart.

"You'll find out, Shadow." Sonic said. "But, I have to ask-"

"I don't have time for you Sonic." Shadow said. "I need to find the rest of the Chaos Emeralds. I have to find out the truth..." He skates away from the blue blur. Sonic watched him going down the city, passing the black creatures.


	3. Chapter 3

***Chapter 2: Sides***

* * *

In the GUN Headquarters, there are men in computers looking through the city that is invaded by the Black Arms, and all the citizens were running from the streets to leave for safety. The Commander stood above the room and watch the screen, and the soldier came in and made a salute.

"The black aliens have hit major cities around the world and every city is reporting significant damage and casualties." He said. The Commander shuts his eyes as he listened. In his mind, he prayed that his family will be safe. Including his daughter-in-law who is 8 months pregnant with a baby boy. And his son is out there fighting the creatures, but haven't heard a word from him since. Then, the soldier continue on with the news. "Downtown Westopolis has been almost completely destroyed. The soldiers were seeing Sonic the Hedgehog helping the citizens to get to safety before getting into a fight, but other than him, they were seeing a black hedgehog in Westopolis."

"Shadow?" The Commander asked, turning his head to the soldier. He now made a snarl. "Deploy the troops, now! And if you find Shadow with the black aliens, then kill them all!"

"But, sir...isn't Shadow on our side?" The soldier asked.

"I gave you an order soldier!" The Commander barked. "He's evil and he's the enemy! Now, go!" The soldier left the room. The Commander clenched his fist in hatred. "You can't fool me, Shadow! This time...you're mine!"

* * *

In Downtown Westopolis, Sonic ran down the streets to see if there are other people who are desperate or injured, but he sees is the GUN soldiers and the black aliens fighting each other. Sonic had never seen anything like this, ever. Fighting Eggman's robots is one thing he knew for years, but now, this is very different, and there's no way that Eggman could be part of this. Wonder if Eggman knew about this?

_"Attention...emergency broadcast to all mobile units... Headquarters to all mobile units."_ A voice from one the soldiers' walkie-talkies. Sonic listened to the Headquarters. _"All points bulletin...be on the lookout for Shadow, the black hedgehog."_

"What?" Sonic asked in confusion. "Why would they want Shadow?"

_"Capture him. Dead or alive."_ The Headquarters said on the talkie. Sonic's ear lowered a bit. He didn't like the sound of the orders. Should he warn Shadow about this?

"Out of my way! Coming through!" A dark voice said. Sonic turned and see Shadow coming towards the soldier who pointed guns at them, but they are afraid of him.

"Stop! Don't move, or...we'll shoot!" One of the soldiers warned nervously. Shadow jumped in the air and knocked out the soldiers flat. Sonic's jaw dropped on the ground. As Shadow landed on the ground with a dark look in his ruby eyes, Sonic approached him with a glare.

"What the hell, man?!" Sonic asked. "Why did you knock them out?!"

"They're in my way, Sonic! Now, if I were you, I'd be on my way so I won't get my ass beaten." Shadow said. Sonic clenched his fists.

"Shadow, these people haven't done anything to you! They need our help!" He said. "We saved Earth together once, and-"

"Shut up, you blue idiot!" Shadow yelled, making Sonic step back a bit. "My memories had nothing to do with you! All I see is a little girl named Maria in my mind, and I don't know who she is and all that crap! So, don't make up the stories about you and me! Got it?!"

"I was just trying-" Sonic stopped when he saw a hologram of the leader of the black aliens. Shadow turned to see Black Doom. "What the...?" Sonic gasped.

"Do not waste your time, Shadow! Find more Chaos Emeralds, and be sure none of those humans have them." He said.

"Who are you?" Shadow asked. "I know you know the truth about my past! You know me, don't you?"

"Hmmm. Just as I thought. Professor Gerald had done something in your memory. But, I am guessing you don't remember your maker either. Am I correct?" Black Doom suggested.

"Professor who?" Shadow asked in confusion. Something about that name is very familiar, same goes with Maria. Sonic got in front of the hologram.

"Just so you know, Mister Alien Boss!" He started. "Shadow had lost his memory for a long time now, and he triggering one! God knows when will his memories will come back to him, but I know he will remember everything! Shadow is a good guy! And he will help me and my friends save the world! Right, Shadow?" He turned to Shadow who looked down at the ground in silent. But, Black Doom spoke.

"If what was the blue hedgehog is saying is true, then your memories will come in time. But now, your mission starts here." He says. Before any of the hedgehogs could react, Black swung his arm and everything went white. Sonic shield his eyes and the light fades away. The hologram and Shadow are gone.

"Huh? Shadow? Shadow, where are you?" He called in thin air. "I hope you know what are you doing!"

* * *

Meanwhile, Eggman is watching the screen in silent and tapping his foot. His robots were behind him in confusion, and Orbot and Cubot were beside him watching the screen. They're watching the footage of the black aliens destroying the city, and the G.U.N. soldiers try to fight them off.

"Those idiots!" Eggman growled. "They're destroying everything! How can I take over the city and build an Eggman Empire if there is no city?!"

"What can we do, doctor?" Cubot asked. Eggman placed his hands on the keyboard.

"I'm at my limit. I have no choice! Send in the Eggman Fleet!" He ordered.

"You mean we have to fight those aliens! There are thousands of them!" Orbot said. "And, I thought we're going to take over the world-"

"Didn't you all idiots hear me?!" Eggman yelled. "Charge!" His robots ran out of the room in a hurry and have to get all the battleships ready. Eggman turned to the screen and found the floating ancient fortress. He can see the black aliens, and the leader of them, but other than them, he sees Shadow with the leader. "Shadow? What is he doing there with those aliens?!" Eggman wondered. Orbot and Cubot looked at the screen as well.

"Oh my! It's been a while since we see that hedgehog! I wonder if he had his memory back?" Orbot exclaimed.

"Oh please, he never remembers us! I doubt he'll get his memory back." Cubot said crossing his arms.

"Why are you two still here?!" Eggman snapped, making his robot sidekicks jump a bit. "Go to the fleet now! I'll send one of my flying monitors out there. Maybe Shadow would love to help me fight the aliens and I will help him in return..." He smiled evilly at himself as he watches Shadow on the screen. He then began to laugh a bit.


	4. Chapter 4

***Chapter 3: Encounters***

* * *

The White House is outside the city that's been invaded. The president was watching the city filled with darkness in his office. He is very worried about the citizens who are out here. Sonic and his team will save them and put them in a save zone for G.U.N. and kill the black aliens. But, why are they here? To take over the planet? They are, of course, twice as worse as Eggman. The beep sounds came from the phone on the desk. A secretary spoke.

_"Mr. President. We've received a report from the Central Information Agency. Our ground troops have successfully pushed back the black aliens from Westopolis." _She said. The president came over to his desk and listened more. _"We've also managed to suppress enemy forces in five other cities. Many of the citizens have been injured, but recently rescued by the military and Sonic the Hedgehog's allies. Few people have been killed, and children have been taken away for medical attentions."_ The president pressed the button to speak to his secretary.

"Tell the Commanding Generals that the United Federation will never surrender to terrorists. And have them keep the survivors safe in the zone, and find the ones out there." He said. He looked at the photo of Sonic and Shadow in front of the White House. Sonic had a grin on his face and his thumb up, and Shadow had his back on the camera, but his head turned with arms crossed. It was the day when Shadow was forced to be in the party with Sonic to celebrate the year of saving Earth from being destroyed a year ago, but Shadow doesn't remember that at all. The president couldn't blame him after the fall of death, but he always wondered how Shadow is alive. Once his memory returns, he will know that he is a hero along with Sonic. And today, they both will save the planet again.

* * *

Everything was so quiet around him. He opened his eyes, trying to regain his vision. Shadow groaned and held his head. He remembered he was teleported with Black Doom from the city. Shadow realized he's alone. Sonic's not here. But, he's no important to the black hedgehog now.

"Where am I?" Shadow asked himself as he stood up. He looked around and found out that he's in the ruins. Torches are lit up, and a temple is far ahead of him. "Whoa... I guess I underestimated his powers." Shadow says. He then hears faint shooting ahead. Could it be those black aliens again? All the way out here? Shadow had to find out what the aliens are up to. He skated off the steps and jump on the ruins to get across. Below him is a lake, and the fall is pretty deep. Anyone could die. Shadow found out where the gunshots came from. He can see the black aliens roaming around, shooting at the G.U.N. soldiers. Shadow knew he couldn't be sighted by one of the soldiers as he goes further. But he hears one of the soldiers cry out.

"There he is! Shoot him!" He says. Shadow skates in full speed to lose the sight of the soldiers and he can hear the cries of agony from them. Sounds like they're getting shot by the aliens. Appearing in front him is Doom's Eye. Shadow stopped in an instant, almost bumping into it. This is Black Doom's third eye from before.

"Are you awake, Shadow?" Doom's Eye asked. "These foolish humans somehow got a track of you here. Kill them when they get in our way."

"Why am I here?" Shadow asked with a look. "What are we doing out here in the ruins?" He can hear the creature chuckle a bit. "What the hell's so funny?"

"Come, Shadow. I will take you to the temple." Doom's Eye says as it flies ahead of Shadow who watched in confusion. "Do you still have those Chaos Emeralds from the city, Shadow? You only have five remaining." Doom's Eye says as it turns to give Shadow the eye. Shadow took out the blue one and a green one.

"...Why do you need them? And what 'promise' do you mean?" Shadow asked. Doom's Eye flew off without saying a word. Shadow puts away the Chaos Emeralds and decided to follow the creature. Black Doom knows something. He had the answers of Shadow's past. He did mention someone by the name of Professor Gerald. That name never rings a bell in Shadow's head.

"Hurry, Shadow! Do not keep us waiting!" Black Doom's voice demanded. Shadow follows Doom's Eye again to get to the temples. Shadow has a job to do. Find the rest of the Chaos Emeralds, and recover his memories. And he will find out what Black Doom and his race are planning.

* * *

Inside the safe zone outside the city, there is a big shelter full of people who are injured. Children were crying, and their mothers try to comfort them. Doctors and nurses are around the injuries in each room. A pink hedgehog and a little rabbit came in with a pregnant woman who held her stomach, feeling her baby move.

"This way, Arianna." Amy says, pulling the woman towards the door where the room with five woman inside, getting bandages from doctors. Amy told Cream to check on the others while he helps Arianna sit on the bean bag. "We're safe here. But, I have to go help Sonic out there to find the other people who need help." She says.

"Thank you, Amy. And if you see my husband, tell him to come here. I'm...worried about him." Arianna said as she strokes her stomach. "He's Lucas Anderson." Amy smiled at her.

"I will. And I'm sure he's still out there fighting those awful aliens." She said. "But now, you need to rest. You could hardly walk when Cream and I took you all the way here." Arianna smiled at the pink hedgehog and lay her head against the wall. "How's your baby in there? Is he kicking?" Arianna nodded a bit.

"Yes he is. I'm...trying to calm him down." She replied, rubbing her stomach. "I hope we win this war, because my baby boy will be born in a month. I don't want my baby to see this..." Amy patted her shoulder before leaving the room. She meets Cream and Cheese in the lobby and found Vanilla coming over with a bag full of medicine and first-aid kits. Coming in is Sonic and Tails, unharmed. Amy came to Sonic with worry, but the blue hedgehog assured her that he is fine, but he did have a scratch on his shoulder.

"Sonic, you're bleeding. You need to clean that up." Vanilla says by taking out the bandages.

"I'm fine, you guys. Really." Sonic said. "Tails and I just came by after we heard you all are here. I wanted to make sure you ladies are okay." Amy, Cream, and Vanilla smiled at him. Tails sat in the corner with a sigh. "Tails and I fight our way here, so...it's tiring." Sonic said. Vanilla placed a bandage on Sonic's shoulder, after she did, Sonic was about to head back out.

"Wait, where are you going?" Amy asked. "You just got here. You need to rest."

"I'm going to the G.U.N. Headquarters. I want to know what they want with Shadow. They're after him." Sonic replies before he dashed out the door. Just before Amy could come after him, Tails ran out the door.

"You guys! Wait!" Amy says as she grabbed her hammer. "I'm coming with you!"

"Amy, no! It's too dangerous!" Vanilla cried out. But the pink hedgehog ran out the door to catch up on Sonic and Tails.

* * *

On the flying fortress from the ruins, Shadow is on top with Black Doom with his arms crossed, spikes rippling behind him. They are in the high blue sky from the grounds, and clouds pass through them. Black Doom told the black hedgehog that he and the Black Arms transported the flying fortress to this planet over 2,000 years ago. It could impose any terror in unimaginable ways to anyone. Shadow seemed to be impressed about it, but never wanted to tell that to Black Doom. But then, there is a red flying ship coming towards the fortress.

"Hmm. Do these fools really believe they could stop..._me_?" Black Doom asked with a dark chuckle. Shadow looked ahead of him and recognize the ship. There is a logo.

"Isn't that...the doctor?!" He asked. He turned back to the leader, but Black Doom is disappearing.

"Destroy the foolish human. Shadow, do not fail me." He says in thin air. Shadow turned back to the ship. Maybe Eggman knows something about the Black Arms. But, will the evil doctor tell him? Shadow remembered 6 months ago when he encountered Eggman at the casino...

* * *

**_*6 months ago*_**

_Eggman was flying with his mobile as he saw Team Dark below him on the platform. Before he could summon his robots, Shadow came up, asking so many questions._

_"Doctor, tell me. What was I doing? Asleep in that base? And what about my memory?" He asked. He heard Eggman huffed a bit._

_"Your memory? What memory?" He lied. "You have no past to remember."_

_"What?"_

_"Well, I believe our time is up." Eggman says. The robots appeared around Team Dark. Omega took out his cannons to aim, and Rouge got in her fighting stance. "We'll meet up again...soon." Eggman flees before Shadow calls out for him._

_"It's no use, Shadow. But we will catch him next time. Now, come on! Let's finish off these robots!" Rouge suggests the black hedgehog. Omega shoots the robots. Shadow didn't do anything to help his friends. He keeps hearing those words in his head. Was Eggman lying to him, or could he possibly telling him the truth? Shadow's been asleep for God knows how long. He couldn't remember what happened last. Rouge knew him from sometime ago, and Eggman knew him as well. Only Eggman knows the truth, and never wanted Shadow to know about it.  
_

* * *

_"Hoho, Shadow! Fancy running into you here!"_ A fuzzy voice said, making Shadow blink. A flying computer screen was in front of him, and there is Eggman on screen with a grin. With him, there is Orbot and Cubot. _"Aren't you here to stop those black creatures?"_ Eggman asks. Shadow glared at the screen.

"Maybe, or maybe not, doctor." He says in a dark tone. "Since you are here, how about you tell me about my memory? If you refuse to tell me, I will follow Black Doom's orders. To destroy you with my bare hands." Orbot and Cubot shook a little.

_"Ohh, doctor, it's best to tell him! He will kill us!"_ Cubot says. Eggman smacked him and turned back to Shadow.

_"How about a little deal, Shadow? If you help me, I will tell you every single thing about your memory and we will find out what these black aliens want."_ He said. _"And I do need all the help. The black creatures are destroying everything!"_ Shadow crossed his arms, giving him a cold eye. Eggman crossed his heart. _"Believe me, Shadow. I will tell you everything you wish to know. I promise."_ Shadow didn't give him a reply, but did give the doctor a nod. Shadow skates off as the computer screen follows him. _"Now Shadow, you must destroy the cores that makes every fortress fly. Afterwards, come to my ship."_ Eggman said. One of the ships besides them explodes, and Shadow took cover behind the pillar. One of the flying aliens roared above.

_"What was that?!" _Orbot asked.

_"It's those black aliens. Shadow, take them down!"_ Eggman ordered. But Shadow spotted Doom's flying about. One of the aliens got a hold of the yellow Chaos Emerald. Shadow skates off to get it from it. _"Shadow! Where are you going?! Shadow!"_ Eggman called, but the black hedgehog didn't hear him. Shadow climbed on the ruins and kicked one of the robots away from him.

_"He's on their side!"_ Cubot said. Eggman growled. The computer screen flew off. Shadow snatched the emerald away from the alien and skates off. He had to be away from the war. Explosions are here and there, and Shadow is too fast for them. He reached on top of the other fortress and raised a Chaos Emerald.

"Chaos Control!" He shouted. Light appears around him, and he disappeared.


	5. Chapter 5

***Chapter 4: Memory of Return***

* * *

A bright light appeared in the room of the deck, and Shadow landed on the floor, making Orbot and Cubot shriek in shock. They backed away as Shadow gave them a look, and Eggman turned to face the black hedgehog. The war is still happening outside, but Shadow only arrived because he wanted answers from Eggman who promised him to tell him about his past.

"Hello, Shadow." Eggman said. "Nice of you to drop in."

"Alright, doctor. You said that you will tell me about my past." Shadow said with a look. "Why should I not to trust Black Doom? He seems to know about me and my past a lot more than you do."

"Oh Shadow, just because someone knows a lot about you doesn't mean they know every single thing about your past." Eggman said. Shadow glared at him. The scientist turned back to the window to see the war. "But, I said I will tell you everything if you help me. Stop Black Doom, and I will tell you the truth about your past." Shadow doesn't know what to do now. First from the city, and now up in the skies? Eggman may not be the most trustful man, but...he knows something and Shadow knows it. But, what about Black Doom? They both seem to know.

"I think I can manage, doctor." Shadow said. "But, if you lie to me..." He came close to Eggman with the most threatening look. "I _will_ find you." Orbot and Cubot shook a little. But Eggman didn't show any fear to the black hedgehog.

"Thank you, Shadow. Now...destroy them. I will guide you." He said. Shadow uses a Chaos Emerald to disappear. The two robots went up to Eggman.

"Doctor! Are you sure this is a good idea?!" Cubot asked.

"Yes. Shadow will do anything to get answers. And...he will be by my side like before..." Eggman said with smirk. "Such a naïve little hedgehog he is."

* * *

Meanwhile, Tails is flying his Tornado in the sky and saw the city in peril. He was avoiding the flying aliens who are after him, but Tails shoots them with his missiles. The fox boy was looking for Sonic and the others to bring them to the safe zone, but he heard that Knuckles was still on Angel Island guarding the Master Emerald from the Black Arms. As Tails flies his plane, he sees the island in the ocean.

"Knuckles!" He called out. He lands his plane on the ground of the island and started to look for the red echidna. "Knuckles? Knuckles, where are you? It's me! Tails!" A roar was heard behind him and Tails backed away in fear as the alien came up to him with a purple sword. As it raises the sword, a fist punch came in to knock the creature down. A red echidna landed on him to knock the alien out. Tails stood up.

"That was a close one." Knuckles said. He turned to his young friend. "You okay, buddy?"

"I'm fine. What about you? Are you okay?" Tails asked.

"Terrific." Knuckles said in a sarcastic tone. "But, I hid the Master Emerald from the temple, thank god."

"They were after it?"

"Not sure, but I have to protect my emerald, no matter what." Knuckles turned to see the city. "Damn. Where do those creatures come from? Is everybody else okay?"

"I'm looking for everyone else. We need to fight those black creatures!" Tails said. "C'mon. Sonic is out there somewhere. He could be in serious trouble. The last time we saw him is from the safe zone where everyone is."

* * *

Shadow appeared on an island. But, not just some island. It's Prison Island that was rebuilt a year ago after the incident. The black hedgehog looked around in silent until memories appear in his head. Memories of him, Eggman, and Rouge on this island for stealing the three Chaos Emeralds. But, for what purpose?

"Uggh..." Shadow grunted as he held his head. Memories of him being awakened by Eggman, fighting Sonic in the woods, saving Rouge from the room, and the island explodes. Shadow opened his eyes. "What?" He looked around again. "This place...I've been here before. This is...Prison Island. I somehow escaped. Eggman has awakened me from this island, and...I have a purpose." As he talked to himself, noises were heard from the bushes. Shadow turned and got into his fighting stance, preparing to fight whoever is watching him. Coming out is Rouge. "Huh?"

"Shadow?" Rouge asked. "Wasn't expecting you here."

"What are you doing out here?" Shadow asked, putting his arms down. Rouge looked around.

"Hiding from those aliens." She whispered. "One of the Chaos Emeralds was held here, but those aliens are after it. I couldn't risk going out there. Who knows what they will do to me." Shadow walk by her and look over the bushes to see the Black Arms roaming around the woods. Rouge was by him. "Think you can take them out?" She asked.

"I could, but...I'm here to seek the truth about my past. I need to find the Chaos Emeralds. The doctor promised me to tell me the truth once I help him." Shadow said. "Black Doom is the leader of the alien race, and...he seems to know me quite well. He said something about Professor Gerald." Rouge stares at her friend.

"Do you remember that name yet?"

"...No. Never ring a bell. But...these memories..." Shadow paused when he remembers. "I was...here before. Awakened by the doctor. We were here to find the emeralds, and Sonic was there...but before those moments, I have...the past. With this girl...Maria."

"So...you're starting to remember almost everything? Your past?" Rouge asked. Shadow nodded a little. Rouge looks down at the ground, pacing a little. She remember when she found the room filled with the Shadow Androids. And she doesn't know for sure if this Shadow she knew was the real one. Shadow started to remember her, and no android can do that. "Hey, Shadow..." Rouge started but the Black Arms appeared from the bushes and about to attack Rouge. Shadow uses Chaos Spear to shock the aliens, and they back down.

"Rouge, run!" Shadow said. Rouge uses her wings to fly off. Shadow attacks the aliens with his feet and fists. When they were down, Doom's Eye appears.

"What are you doing, you traitor?!" He asked. "Those are our soldiers, Shadow!" Shadow scoffed and about to walk away, but Doom's Eye flew in front of him to stop him. "One Chaos Emerald was held by those human machines, Shadow. Get it now!"

"I don't take orders." Shadow said and skates off. Doom's Eye watched the black hedgehog flee. He made a sound of thought.  
Shadow snuck in the prison to get the Chaos Emerald from the vault. Thanks to Rouge who shows him how to crack a code, the vault opens. As he reaches for the emerald, head began to hurt.

"Uggh!" He grunted and got on his knees, holding his head. "Dammit!"

* * *

_***6 months ago***_

_He opened his eyes, and there was Rouge backing away in shock. She awakens him. But, they are not alone. Out of the shadows is E-123 Omega, he began to shoot the room, but he's aiming for Shadow. The black hedgehog leaped out of the pod and push Rouge out of the way.  
_

_"Stay here!" He told her and jump on the walls to stall Omega from hurting Rouge._

_"Shadow?!" Rouge cried out. _

_**"MUST ELIMENATE ALL EGGMAN ROBOTS!" **Omega spoke in a robotic voice, trying to shoot Shadow who is dodging his bullets. Rouge turned to Omega in confusion. Omega wasn't trying to kill her or Shadow. He's against Eggman and his robots. But why? Shadow ducked behind the pod and went around to charge at Omega. Rouge came in between them._

_"Hey, hold up!" She yelled. The two backed away in silent. Rouge sighed a little, she faces Shadow. "He's not going to hurt us, Shadow. He's against Eggman..." Shadow gave her a strange look and cock his head to the side._

_"...How do you know my name?" He asked. Rouge blinked. "Who are you?"_

_"Huh?"  
A few minutes, Rouge figured everything out for both Shadow and Omega. The reason why Omega was angry at Eggman for sealing him up in this room. And Shadow doesn't remember anything. But still, Rouge was surprised to see Shadow alive. How is that possible? Eggman must know something._

_"Then it's settled!" Rouge spoke. She got the two come to her. "Now you two make up, because we're going after Eggman. Together." Shadow didn't say anything to her, and neither does Omega. Rouge smiled at them for not trying to kill each other. "Oh yeah, baby! This makes us a team!"  
_

* * *

"Shadow...Shadow..." A deep voice said. Shadow groaned a little and opened his eyes to see Doom's Eye floating around him. "Get up, Shadow. You have a next mission. You only have four Chaos Emeralnds left to obtain." Shadow got up, and he is still on Prison Island. A white Chaos Emerald is by his feet. He picked up and look up at Doom's Eye._  
_

"Tell me something." He said. "Why do you need them?"

"To help you, Shadow." Doom's Eye spoke. "You want to know about your past, don't you? I know everything... Do not trust those foolish humans or the blue hedgehog's friends. Especially that doctor. If you work with him, he will slow you down."

"He knows about me." Shadow said. Doom's Eye chuckled. "What?"

"Would you believe that you are an...android like his creations?"

"...Huh?"

"Believe the doctor who 'knows' everything about your past. Or find me the Chaos Emeralds as promised. I will tell you everything." Doom's Eye said. "We have one of the emeralds we have found, but you will only find the rest."

"So...three more." Shadow said. "You're saying that I shouldn't trust Eggman? Hmm..."

"Now go. My army will take you to the leader's area." Doom's Eye said and it flew off. Before Shadow could speak again, one of the flying aliens came to him. Shadow climbed on and took off with it. The flying creature soar up to the sky as Shadow held on the spikes.


	6. Chapter 6

***Chapter 5: Heartless...***

* * *

At the G.U.N. Headquarters, the Commander was on the talkie with his daughter-in-law who is in the safe zone with the rest. The Commander was relieved that Arianna is safe, but her husband wasn't around yet. And that made the Commander worry. His son is either in the city or elsewhere that is very unsafe. Coming in is Sonic and Espio with the soldier. They saluted to him.

"Sir, Sonic the Hedgehog and Espio the Chameleon are here in once piece." The soldier said before leaving the room. The Commander turned to him and saluted to them as well, and lower his arm. Sonic and Espio don't look harmed, but Sonic does have a small cut on his arm.

"Sonic and Espio. Thank god, you two made it safe." The Commander said. "You have your team all together?"

"Almost. There's Rouge, and Vector." Sonic said.

"I couldn't find Vector anywhere, but I know he will be coming by the safe zone. And Rouge is a strong bat." Espio said. "And no sign of Shadow anywhere." The Commander growled a little. "Sir? Are you alright?"

"That hedgehog is siding with those aliens." The Commander said. "I know it."

"Huh? Shadow with those black aliens? No way." Sonic said doubtfully. "The last time I saw him was in the city, and then he was gone."

"Sonic, no matter what you do, you have to stop Shadow." The Commander said. "He's evil, and very dangerous to the world." Sonic didn't say anything. He couldn't argue with the Commander. Maybe Sonic will try to talk to Shadow if he can find him before anything happens. "And bring him to me. Dead or alive." The Commander said. The blue hedgehog couldn't say no to the Commander. He had to do it to save the planet.

"Sure." Sonic said in a whisper.

"Sir, I will keep in contact with you at the safe zone, but I will have to look for Vector. I will keep those aliens away from the zone for you." Espio said by taking out his knives. "We can win this war."

"When my soldiers return in one piece, we will kill those creatures." The Commander said. "But, we need to bring the President here. He could be in grave danger..." He turned to Sonic. "Will you come with me and my men to the White House to get the President, Sonic? We could use some help."

"Yes, sir." Sonic said with a nod. He walked out the door with Espio, and he stopped in the middle of the corridor. Espio turned back to him in concern. Sonic looked up at the chameleon. "Espio, you don't think that...Shadow is a bad guy, do you?" He asked. "Because...he was confused and his memory was lost. Why would Shadow be on the aliens' side?"

"We don't know for sure, Sonic." Espio said. "We will find him and get answers from him. I'll meet you back the safe zone with the others later." He ran down the corridor, leaving the blue hedgehog behind. Sonic was deep in thought. What should he do? Talk to Shadow, or bring Shadow here in the Headquarters of G.U.N.?

"Oh dammit, what should I do?" Sonic says to himself as he left the headquarters.

* * *

In the skies, Shadow was on the Black Hawk, gripping on the spikes and found the flying fortress and the Egg Fleet. There are more Black Hawks flying around with sounds. Shadow glared at the Egg Fleet and commands the creature to go to it.

"I can't get the rest of the emeralds if that doctor was in our way!" He says. "I have to know the truth about my past." Before he got closer to the Egg Fleet, something hits Shadow's mind. He uses one hand to hold his head, and shut his eyes. Those memories again. He started to remember...he and his team are fighting Eggman on this ship, and then Metal Sonic. He shook his head, focusing on the mission. There is a flying monitor coming towards Shadow.

_"Shadow! What're you doing?! You're on my side now!"_ Eggman said in anger.

"Hmph. I thought about helping you, but I think it's best if I join with Black Doom." Shadow scoffed. The Black Hawk uses his tail to hit the monitor, and Eggman's scream is heard. Shadow uses the creature to head upwards to the top of the ship. Suddenly, the Black Hawk started to screech in agony and started to head down. Shadow gripped on the spikes and look behind him to see the spear on the side. "What the hell?" Shadow wondered and look down to see G.U.N. soldiers shooting the Black Arms from the temples. "Foolish humans." Shadow muttered. He lowers the creature to get down on the temple. Eggman, Black Arms, and G.U.N. are at war, and Shadow had to get out of it. He took out a Chaos Emerald to warp out of the skies.

"Sir, Shadow has escaped!" One of the soldiers said.

_"Find him!" _The Commander's voice said from the talkie. _"I want him found!"_

"He will be found sir!" The soldier said.

* * *

Shadow was wandering to the woods, thinking things over. Everything around him is quiet. No aliens on sight, no war, no soldiers. Shadow places his hand over his head, memories are floating around.

_'What the hell is going on with me? I can't get these images out of my mind. Those black creatures...' _Shadow thought, looking up at the clear sky. _'How do they know me? Who was I before this?' _He then felt a strange energy around him. The forest was growing dark and dim, and a red light appears below his feet. Shadow notices that he is no longer in the woods, he is in space, floating. What just happened?

"Shadow...you seem troubled." A voice said behind the black hedgehog. Shadow turned to see Black Doom.

"You!"

"Look." Black Doom pointed his claw towards a large object. Shadow turned to see a station below him. There is Earth below the station. Shadow couldn't help but to feel connected to this place.

"That's the..."

"Yes, that's right." Black Doom spoke. "The Space Colony ARK. 50 years ago. And you are a part of it."

"The ARK?" Shadow asked, wide eyed. "50...years ago?" He can see the windows of the corridor where he can see a girl with blonde hair running with a black hedgehog. She tripped, but the hedgehog helped her up and continue to run. "That's...me!" Shadow exclaimed. He sees his past self turning his head back, and back to front with the girl. Shadow notices the G.U.N. soldiers chasing after them. Shadow made a look. This is the memory he saw before. This is how Maria died.

"That's right." Black Doom spoke. "This will remind you what the humans did to you. Never forget that horrifying image." He and Shadow disappeared to get inside the ARK that was under attack. They are visiting 50 years ago...


End file.
